18-46665492-C-T

Variant names:

• chr18-46665492-C-T
• rs430374
• XR_935430.4:n.716G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_935430.4(LOC105372096):​n.716G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,014 control chromosomes in the GnomAD database, including 4,637 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4637 hom., cov: 31)
• Consequence: LOC105372096 XR_935430.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 3 publications found

Genes affected

LOC105372096 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36649 AN: 151896 Hom.: 4637 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.241 AC: 36665 AN: 152014 Hom.: 4637 Cov.: 31 AF XY: 0.240 AC XY: 17864 AN XY: 74306

African (AFR) AF: 0.199 AC: 8238 AN: 41470

American (AMR) AF: 0.194 AC: 2968 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.133 AC: 687 AN: 5164

South Asian (SAS) AF: 0.113 AC: 543 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3510 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18783 AN: 67964

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.258 Hom.: 16390

Bravo AF: 0.231

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs430374; hg19: chr18-44245455;